[Background] Virus infects sweet potato plants, and causes serious economic losses frequently in Fujian province. There may exist more than one species of sweet potato virus. [Objective] To determine the sweet potato virus species and prevalence in Fujian, and analyze the genetic diversity of the main viruses. [Methods] Viruses were isolated from samples with viral diseases symptoms from different sweet potato production areas in Fujian province, 14 pair primers of viruses infecting sweet potato were used to detect by PCR or RT-PCR. The PCR amplicons of SPFMV (sweet potato feathery mottle virus), SPCSV (sweet potato chlorotic stunt virus) and SPLCV (sweet potato leaf curl virus) from selected samples were cloned and sequenced. The alignments and phylogenetic analyses were performed with the MEGA 6.0 software package. [Results] The results showed that 12 virus species were detected infecting sweet potato in Fujian, of which 9 were RNA viruses, including sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), sweet potato virus G (SPVG), sweet potato virus C (SPVC), sweet potato virus 2 (SPV2), sweet potato chlorotic fleck virus (SPCFV), sweet potato latent virus (SPLV), sweet potato mild speaking virus (SPMSV), cucumber mosaic virus (CMV); and three DNA viruses including sweet potato leaf curl virus (SPLCV), sweet potato symptomless virus 1 (SPSMV-1), sweet potato badnavirus B (SPBV-B). Among 179 sweet potato samples, SPFMV was detected in 90 samples (50.28%), SPCSV was detected in 75 samples (41.90%), SPVG in 64 samples (35.75%), SPVLCV in 44 samples (24.58%), and CMV just in five sample (2.79%), however, no samples infection was detected for SPV-2 and SPMMV. Mixed infections of 2–6 viruses were common (85.61%) in Fujian. The analysis of phylogenetic relationships showed that SPFMV isolates mainly belong to strains of EA, O and RC, SPCSV isolates mainly belong to strains of WA, and SPLCV isolates were divided into two groups. [Conclusion] There were many sweet potato viruses with complex infection models and genetic diversity were proved in Fujian province.